1
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Keeley A, Kopranovic A, Di Lorenzo V, Ábrányi-Balogh P, Jänsch N, Lai LN, Petri L, Orgován Z, Pölöske D, Orlova A, Németh A, Desczyk C, Imre T, Bajusz D, Moriggl R, Meyer-Almes FJ, Keserü GM. Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors. J Med Chem 2024; 67:572-585. [PMID: 38113354 PMCID: PMC10788917 DOI: 10.1021/acs.jmedchem.3c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Screening of ultra-low-molecular weight ligands (MiniFrags) successfully identified viable chemical starting points for a variety of drug targets. Here we report the electrophilic analogues of MiniFrags that allow the mapping of potential binding sites for covalent inhibitors by biochemical screening and mass spectrometry. Small electrophilic heterocycles and their N-quaternized analogues were first characterized in the glutathione assay to analyze their electrophilic reactivity. Next, the library was used for systematic mapping of potential covalent binding sites available in human histone deacetylase 8 (HDAC8). The covalent labeling of HDAC8 cysteines has been proven by tandem mass spectrometry measurements, and the observations were explained by mutating HDAC8 cysteines. As a result, screening of electrophilic MiniFrags identified three potential binding sites suitable for the development of allosteric covalent HDAC8 inhibitors. One of the hit fragments was merged with a known HDAC8 inhibitor fragment using different linkers, and the linker length was optimized to result in a lead-like covalent inhibitor.
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Affiliation(s)
- Aaron
B. Keeley
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Aleksandra Kopranovic
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Vincenzo Di Lorenzo
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Niklas Jänsch
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Linh N. Lai
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - László Petri
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Daniel Pölöske
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna Orlova
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - András
György Németh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Charlotte Desczyk
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Tímea Imre
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- MS
Metabolomics
Research Group, Research Centre for Natural
Sciences, Magyar tudósok
krt 2, H-1117 Budapest, Hungary
| | - Dávid Bajusz
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Richard Moriggl
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Franz-Josef Meyer-Almes
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - György M. Keserü
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
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2
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Orgován Z, Péczka N, Petri L, Ábrányi-Balogh P, Ranđelović I, Tóth S, Szakács G, Nyíri K, Vértessy B, Pálfy G, Vida I, Perczel A, Tóvári J, Keserű GM. Covalent fragment mapping of KRas G12C revealed novel chemotypes with in vivo potency. Eur J Med Chem 2023; 250:115212. [PMID: 36842271 DOI: 10.1016/j.ejmech.2023.115212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
G12C mutant KRas is considered druggable by allele-specific covalent inhibitors due to the nucleophilic character of the oncogenic mutant cysteine at position 12. Discovery of these inhibitors requires the optimization of both covalent and noncovalent interactions. Here, we report covalent fragment screening of our electrophilic fragment library of diverse non-covalent scaffolds equipped with 40 different electrophilic functionalities to identify fragments as suitable starting points targeting Cys12. Screening the library against KRasG12C using Ellman's free thiol assay, followed by protein NMR and cell viability assays, resulted in two potential inhibitor chemotypes. Characterization of these scaffolds in in vitro cellular- and in vivo xenograft models revealed them as promising starting points for covalent drug discovery programs.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary
| | - Nikolett Péczka
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - Szilárd Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kinga Nyíri
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
| | - Beáta Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
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3
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Kiss-Szemán AJ, Takács L, Orgován Z, Stráner P, Jákli I, Schlosser G, Masiulis S, Harmat V, Menyhárd DK, Perczel A. A carbapenem antibiotic inhibiting a mammalian serine protease: structure of the acylaminoacyl peptidase-meropenem complex. Chem Sci 2022; 13:14264-14276. [PMID: 36545146 PMCID: PMC9749117 DOI: 10.1039/d2sc05520a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022] Open
Abstract
The structure of porcine AAP (pAAP) in a covalently bound complex with meropenem was determined by cryo-EM to 2.1 Å resolution, showing the mammalian serine-protease inhibited by a carbapenem antibiotic. AAP is a modulator of the ubiquitin-proteasome degradation system and the site of a drug-drug interaction between the widely used antipsychotic, valproate and carbapenems. The active form of pAAP - a toroidal tetramer - binds four meropenem molecules covalently linked to the catalytic Ser587 of the serine-protease triad, in an acyl-enzyme state. AAP is hindered from fully processing the antibiotic by the displacement and protonation of His707 of the catalytic triad. We show that AAP is made susceptible to the association by its unusually sheltered active pockets and flexible catalytic triads, while the carbapenems possess sufficiently small substituents on their β-lactam rings to fit into the shallow substrate-specificity pocket of the enzyme.
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Affiliation(s)
- Anna J. Kiss-Szemán
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary
| | - Luca Takács
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Pál Stráner
- ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Imre Jákli
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Gitta Schlosser
- ELKH-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Eötvös Loránd UniversityBudapestHungary
| | - Simonas Masiulis
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenThe Netherlands
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
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Abstract
INTRODUCTION Covalent drugs have been used for more than hundred years, but gathered larger interest in the last two decades. There are currently over a 100 different electrophilic warheads used in covalent ligands, and there are several considerations tailoring their reactivity against the target of interest, which is still a challenging task. AREAS COVERED This review aims to give an overview of electrophilic warheads used for protein labeling in chemical biology and medicinal chemistry. The warheads are discussed by targeted residues, mechanism and selectivity, and analyzed through three different datasets including our collection of warheads, the CovPDB database, and the FDA approved covalent drugs. Moreover, the authors summarize general practices that facilitate the selection of the appropriate warhead for the target of interest. EXPERT OPINION In spite of the numerous electrophilic warheads, only a fraction of them is used in current drug discovery projects. Recent studies identified new tractable residues by applying a wider array of warhead chemistries. However, versatile, selective warheads are not available for all targetable amino acids, hence discovery of new warheads for these residues is needed. Broadening the toolbox of the warheads could result in novel inhibitors even for challenging targets developing with significant therapeutic potential.
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Affiliation(s)
- Nikolett Péczka
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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5
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Abstract
Metabotropic glutamate receptors (mGlu) are class C G protein-coupled receptors of eight subtypes that are omnipresently expressed in the central nervous system. mGlus have relevance in several psychiatric and neurological disorders, therefore they raise considerable interest as drug targets. Allosteric modulators of mGlus offer advantages over orthosteric ligands owing to their increased potential to achieve subtype selectivity, and this has prompted discovery programs that have produced a large number of reported allosteric mGlu ligands. However, the optimization of allosteric ligands into drug candidates has proved to be challenging owing to induced-fit effects, flat or steep structure-activity relationships and unexpected changes in theirpharmacology. Subtle structural changes identified as molecular switches might modulate the functional activity of allosteric ligands. Here we review these switches discovered in the metabotropic glutamate receptor family..
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
| | - György M. Keserű
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
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6
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Abstract
RAS proteins control a number of essential cellular processes as molecular switches in the human body. Presumably due to their important signalling role, RAS proteins are among the most frequently mutated oncogenes in human cancers. Hence, numerous efforts were done to develop appropriate therapies for RAS-mutant cancers in the last three decades. This review aimed to collect all of the reported small molecules that affect RAS signalling. These molecules can be divided in four main branches. First, we address approaches blocking RAS membrane association. Second, we focus on the stabilization efforts of non-productive RAS complexes. Third, we examine the approach to block RAS downstream signalling through disturbance of RAS-effector complex formation. Finally, we discuss direct inhibition; particularly the most recently reported covalent inhibitors, which are already advanced to human clinical trials.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary.
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7
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Abstract
Oncogenic RAS proteins, involved in ∼30% of human tumors, are molecular switches of various signal transduction pathways. Here we apply a new protocol for the NMR study of KRAS in its (inactive) GDP- and (activated) GTP-bound form, allowing a comprehensive analysis of the backbone dynamics of its WT-, G12C- and G12D variants. We found that Tyr32 shows opposite mobility with respect to the backbone of its surroundings: it is more flexible in the GDP-bound form while more rigid in GTP-complexes (especially in WT- and G12D-GTP). Using the G12C/Y32F double mutant, we showed that the presence of the hydroxyl group of Tyr32 has a marked effect on the G12C-KRAS-GTP system as well. Molecular dynamics simulations indicate that Tyr32 is linked to the γ-phosphate of GTP in the activated states – an arrangement shown, using QM/MM calculations, to support catalysis. Anchoring Tyr32 to the γ-phosphate contributes to the capture of the catalytic waters participating in the intrinsic hydrolysis of GTP and supports a simultaneous triple proton transfer step (catalytic water → assisting water → Tyr32 → O1G of the γ-phosphate) leading to straightforward product formation. The coupled flip of negatively charged residues of switch I toward the inside of the effector binding pocket potentiates ligand recognition, while positioning of Thr35 to enter the coordination sphere of the Mg2+ widens the pocket. Position 12 mutations do not disturb the capture of Tyr32 by the γ-phosphate, but (partially) displace Gln61, which opens up the catalytic pocket and destabilizes catalytic water molecules thus impairing intrinsic hydrolysis. Nucleotide exchange to the physiological, activated, GTP-bound form of KRAS results in the anchoring of Tyr32 within the active site.![]()
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Affiliation(s)
- Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
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8
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Nyíri K, Koppány G, Pálfy G, Vida I, Tóth S, Orgován Z, Ranđelović I, Baranyi M, Molnár E, Keserû MG, Tóvári J, Perczel A, Vértessy BG, Tímár J. [Allele-specific inhibitors of mutant KRAS are in the focus of RASopathy consortium]. Magy Onkol 2019; 63:310-323. [PMID: 31821386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The RASopathy consortium was built from research groups of the Budapest University of Technology and Economics, Eötvös Loránd University, Semmelweis University and two startups: KINETO Lab Ltd. and Fototronic Ltd. The goal was to design and test novel covalent and allele-specific KRAS small molecular inhibitors. KRAS is the most frequently mutated human oncogene which was unsuccessfully targeted until recently. The consortium established G12C-expressing bacterial and human cancer cell models (homo- and heterozygous variants) of lung, colorectal and pancreatic tumors. Using covalent fragment and acrylamide warhead libraries we were able to select novel candidates of small molecular G12C-specific inhibitors which were compared to published best-in-class drug candidates.
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Affiliation(s)
- Kinga Nyíri
- Alkalmazott Biotechnológiai és Élelmiszertudományi Tanszék, BME, Természettudományi Kutatóközpont, Budapest, Hungary
| | - Gergely Koppány
- Alkalmazott Biotechnológiai és Élelmiszertudományi Tanszék, BME, Természettudományi Kutatóközpont, Budapest, Hungary
| | - Gyula Pálfy
- Szerkezeti Kémia és Biológia Laboratórium, Budapest, Hungary
| | - István Vida
- Szerkezeti Kémia és Biológia Laboratórium, Budapest, Hungary
| | | | - Zoltán Orgován
- ELTE Kémiai Intézet, Gyógyszerkémiai Kutatócsoport, Budapest, Hungary
| | | | - Marcell Baranyi
- II. Sz. Patológiai Intézet, Semmelweis Egyetem, Budapest, Hungary.
| | - Eszter Molnár
- II. Sz. Patológiai Intézet, Semmelweis Egyetem, Budapest, Hungary.
| | | | | | - András Perczel
- MTA-ELTE Fehérjemodellezõ Kutatócsoport, Budapest, Hungary
| | | | - József Tímár
- II. Sz. Patológiai Intézet, Semmelweis Egyetem, Budapest, Hungary.
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9
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Orgován Z, Ferenczy GG, Keserű GM. Fragment-Based Approaches for Allosteric Metabotropic Glutamate Receptor (mGluR) Modulators. Curr Top Med Chem 2019; 19:1768-1781. [PMID: 31393248 DOI: 10.2174/1568026619666190808150039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/03/2019] [Accepted: 07/29/2019] [Indexed: 12/28/2022]
Abstract
Metabotropic glutamate receptors (mGluR) are members of the class C G-Protein Coupled Receptors (GPCR-s) and have eight subtypes. These receptors are responsible for a variety of functions in the central and peripheral nervous systems and their modulation has therapeutic utility in neurological and psychiatric disorders. It was previously established that selective orthosteric modulation of these receptors is challenging, and this stimulated the search for allosteric modulators. Fragment-Based Drug Discovery (FBDD) is a viable approach to find ligands binding at allosteric sites owing to their limited size and interactions. However, it was also observed that the structure-activity relationship of allosteric modulators is often sharp and inconsistent. This can be attributed to the characteristics of the allosteric binding site of mGluRs that is a water channel where ligand binding is accompanied with induced fit and interference with the water network, both playing a role in receptor activation. In this review, we summarize fragment-based drug discovery programs on mGluR allosteric modulators and their contribution identifying of new mGluR ligands with better activity and selectivity.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
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10
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Orgován Z, Ferenczy GG, Keserű GM. The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu 5 receptor case study. J Comput Aided Mol Des 2019; 33:787-797. [PMID: 31542869 PMCID: PMC6825653 DOI: 10.1007/s10822-019-00224-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022]
Abstract
Stabilizing unique receptor conformations, allosteric modulators of G-protein coupled receptors (GPCRs) might open novel treatment options due to their new pharmacological action, their enhanced specificity and selectivity in both binding and signaling. Ligand binding occurs at intrahelical allosteric sites and involves significant induced fit effects that include conformational changes in the local protein environment and water networks. Based on the analysis of available crystal structures of metabotropic glutamate receptor 5 (mGlu5) we investigated these effects in the binding of mGlu5 receptor negative allosteric modulators. A large set of retrospective virtual screens revealed that the use of multiple protein structures and the inclusion of selected water molecules improves virtual screening performance compared to conventional docking strategies. The role of water molecules and protein flexibility in ligand binding can be taken into account efficiently by the proposed docking protocol that provided reasonable enrichment of true positives. This protocol is expected to be useful also for identifying intrahelical allosteric modulators for other GPCR targets.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary.
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11
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Jójárt B, Orgován Z, Márki Á, Pándy-Szekeres G, Ferenczy GG, Keserű GM. Allosteric activation of metabotropic glutamate receptor 5. J Biomol Struct Dyn 2019; 38:2624-2632. [DOI: 10.1080/07391102.2019.1638302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Szeged, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Márki
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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Christopher JA, Orgován Z, Congreve M, Doré AS, Errey JC, Marshall FH, Mason JS, Okrasa K, Rucktooa P, Serrano-Vega MJ, Ferenczy GG, Keserű GM. Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu5) X-ray Structures. J Med Chem 2018; 62:207-222. [DOI: 10.1021/acs.jmedchem.7b01722] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- John A. Christopher
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest H-1117, Hungary
| | - Miles Congreve
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Andrew S. Doré
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - James C. Errey
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Fiona H. Marshall
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Krzysztof Okrasa
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Prakash Rucktooa
- Heptares Therapeutics Ltd., BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | | | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest H-1117, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest H-1117, Hungary
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13
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Orgován Z, Ferenczy GG, Steinbrecher T, Szilágyi B, Bajusz D, Keserű GM. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors. J Comput Aided Mol Des 2018; 32:331-345. [PMID: 29335871 DOI: 10.1007/s10822-018-0097-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/06/2018] [Indexed: 01/16/2023]
Abstract
Optimization of fragment size D-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | | | - Bence Szilágyi
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary.
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14
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Galambos J, Bielik A, Wágner G, Domány G, Kóti J, Béni Z, Szigetvári Á, Sánta Z, Orgován Z, Bobok A, Kiss B, Mikó-Bakk ML, Vastag M, Sághy K, Krasavin M, Gál K, Greiner I, Szombathelyi Z, Keserű GM. Discovery of 4-amino-3-arylsulfoquinolines, a novel non-acetylenic chemotype of metabotropic glutamate 5 (mGlu 5 ) receptor negative allosteric modulators. Eur J Med Chem 2017; 133:240-254. [DOI: 10.1016/j.ejmech.2017.03.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/09/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
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15
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Galambos J, Bielik A, Krasavin M, Orgován Z, Domány G, Nógrádi K, Wágner G, Balogh GT, Béni Z, Kóti J, Szakács Z, Bobok A, Kolok S, Mikó-Bakk ML, Vastag M, Sághy K, Laszy J, Halász AS, Balázs O, Gál K, Greiner I, Szombathelyi Z, Keserű GM. Discovery and Preclinical Characterization of 3-((4-(4-Chlorophenyl)-7-fluoroquinoline-3-yl)sulfonyl)benzonitrile, a Novel Non-acetylenic Metabotropic Glutamate Receptor 5 (mGluR5) Negative Allosteric Modulator for Psychiatric Indications. J Med Chem 2017; 60:2470-2484. [DOI: 10.1021/acs.jmedchem.6b01858] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- János Galambos
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Attila Bielik
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Mikhail Krasavin
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii Prospekt, Peterhof, 198504 Russia
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest, 1117 Hungary
| | - György Domány
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Katalin Nógrádi
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Gábor Wágner
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | | | - Zoltán Béni
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - János Kóti
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Zoltán Szakács
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Amrita Bobok
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Sándor Kolok
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | | | - Mónika Vastag
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Katalin Sághy
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Judit Laszy
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | | | - Ottilia Balázs
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - Krisztina Gál
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | - István Greiner
- Gedeon Richter Plc, 19-21 Gyömrői
út, Budapest, 1103 Hungary
| | | | - György M. Keserű
- Medicinal
Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest, 1117 Hungary
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Menyhárd DK, Orgován Z, Szeltner Z, Szamosi I, Harmat V. Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. ACTA ACUST UNITED AC 2015; 71:461-72. [PMID: 25760596 DOI: 10.1107/s1399004714026819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/05/2014] [Indexed: 11/10/2022]
Abstract
Acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments. In the case of AAP from Aeropyrum pernix (ApAAP), previous studies have led to a model in which the clamshell-like opening and closing of the enzyme provides the means of substrate-size selection. The closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. The crystallographic results presented here show that the open form of ApAAP is indeed functionally disabled. The obtained crystal structures also reveal that the closed form is penetrable to small ligands: inhibitor added to the pre-formed crystal was able to reach the active site of the rigidified protein, which is only possible through the narrow channel of the propeller domain. Molecular-dynamics simulations investigating the structure of the complexes formed with longer peptide substrates showed that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed; however, their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close.
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Affiliation(s)
| | - Zoltán Orgován
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Ilona Szamosi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Veronika Harmat
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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